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- PDB-5sv0: Structure of the ExbB/ExbD complex from E. coli at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 5sv0
TitleStructure of the ExbB/ExbD complex from E. coli at pH 7.0
ComponentsBiopolymer transport protein ExbB
KeywordsTRANSPORT PROTEIN / ExbB / membrane proteins / pore / channel
Function / homology
Function and homology information


energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport ...energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport / intracellular iron ion homeostasis / protein stabilization / identical protein binding / membrane / plasma membrane
Similarity search - Function
TonB-system energizer ExbB type-1 / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Biopolymer transport protein ExbB / Biopolymer transport protein ExbB
Similarity search - Component
Biological speciesEscherichia coli DH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCelia, H. / Botos, I. / Lloubes, R. / Buchanan, S.K. / Noinaj, N.
Funding support United States, France, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1K22AI113078-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK036139-10 United States
French National Research AgencyANR-14-CE09-0023 France
Projets internationaux de cooperation scientifiquePICS05853 France
CitationJournal: Nature / Year: 2016
Title: Structural insight into the role of the Ton complex in energy transduction.
Authors: Celia, H. / Noinaj, N. / Zakharov, S.D. / Bordignon, E. / Botos, I. / Santamaria, M. / Barnard, T.J. / Cramer, W.A. / Lloubes, R. / Buchanan, S.K.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
E: Biopolymer transport protein ExbB
F: Biopolymer transport protein ExbB
G: Biopolymer transport protein ExbB
H: Biopolymer transport protein ExbB
I: Biopolymer transport protein ExbB
J: Biopolymer transport protein ExbB
A: Biopolymer transport protein ExbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,18915
Polymers263,39410
Non-polymers7955
Water2,558142
1
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
F: Biopolymer transport protein ExbB
A: Biopolymer transport protein ExbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2148
Polymers131,6975
Non-polymers5173
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-120 kcal/mol
Surface area52350 Å2
MethodPISA
2
E: Biopolymer transport protein ExbB
G: Biopolymer transport protein ExbB
H: Biopolymer transport protein ExbB
I: Biopolymer transport protein ExbB
J: Biopolymer transport protein ExbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9757
Polymers131,6975
Non-polymers2782
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-119 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.166, 104.779, 149.364
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Biopolymer transport protein ExbB


Mass: 26339.367 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Gene: exbB / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABU8, UniProt: P0ABU7*PLUS
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAuthors state that all of the experiments indicate that ExbD is present in the structure, but not ...Authors state that all of the experiments indicate that ExbD is present in the structure, but not well ordered. The density for it is not good enough to build into. This happens at neutral pH. However, at low pH, the ExbD helix can be seen clearly. Authors hypothesize that since this complex responds to the proton motive force (proton gradient), the order of the ExbD helix is modulated by pH.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES-NaOH, pH 7.0, 100 mM CaCl2, and 22% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→46 Å / Num. obs: 126321 / % possible obs: 96.3 % / Redundancy: 3.5 % / Rsym value: 0.12 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.2 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
DENZOHKL2000data reduction
SCALEPACKHKL2000data scaling
PHASERPHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.39
Details: Authors state that all of the experiments indicate that ExbD is present in the structure, but not well ordered. The density for it is not good enough to build into. This happens at neutral ...Details: Authors state that all of the experiments indicate that ExbD is present in the structure, but not well ordered. The density for it is not good enough to build into. This happens at neutral pH. However, at low pH, the ExbD helix can be seen clearly. Authors hypothesize that since this complex responds to the proton motive force (proton gradient), the order of the ExbD helix is modulated by pH.
RfactorNum. reflection% reflection
Rfree0.2576 2004 1.59 %
Rwork0.2111 --
obs0.2118 126321 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16649 0 47 142 16838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116953
X-RAY DIFFRACTIONf_angle_d1.1322967
X-RAY DIFFRACTIONf_dihedral_angle_d18.64710076
X-RAY DIFFRACTIONf_chiral_restr0.062721
X-RAY DIFFRACTIONf_plane_restr0.0072959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64070.37381010.34436528X-RAY DIFFRACTION70
2.6407-2.71210.37051480.32758986X-RAY DIFFRACTION96
2.7121-2.79190.35381510.31988959X-RAY DIFFRACTION96
2.7919-2.8820.32011400.30079026X-RAY DIFFRACTION96
2.882-2.98490.31441440.28529075X-RAY DIFFRACTION96
2.9849-3.10440.32121580.2739013X-RAY DIFFRACTION97
3.1044-3.24570.31141370.2599096X-RAY DIFFRACTION97
3.2457-3.41680.31371550.23459090X-RAY DIFFRACTION97
3.4168-3.63070.26211400.21219092X-RAY DIFFRACTION96
3.6307-3.91090.25211660.19339106X-RAY DIFFRACTION97
3.9109-4.30430.23311320.17369081X-RAY DIFFRACTION97
4.3043-4.92650.19471520.16239129X-RAY DIFFRACTION97
4.9265-6.20450.26581410.20799123X-RAY DIFFRACTION96
6.2045-46.33030.21081390.17899013X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.40562.00592.65611.84371.03671.5171-0.3321-0.49771.39450.0474-0.00520.3027-0.1414-0.25320.39360.66710.0587-0.04420.48990.00620.56121.409-3.9731-57.8432
24.0093-1.57665.31645.4773-1.1876.98180.439-0.523-1.22230.4646-0.0981.10330.074-0.9063-0.25980.43280.01560.02540.3845-0.00470.557433.9062-13.6381-55.384
33.75881.56145.13215.73632.08916.66281.467-0.8777-0.28180.2427-0.85640.80891.0132-0.3981-0.39730.4632-0.05870.00040.49870.14641.0083-11.9362-20.6934-72.2703
43.30571.03991.90311.13940.35971.03180.0488-0.07220.69350.0145-0.0920.26830.00070.03530.02120.47220.0102-0.12020.4988-0.06950.595624.6454-8.0556-65.1973
58.21891.27463.53740.43280.46782.4797-0.0548-1.16470.22810.13140.01110.2296-0.007-0.55510.05390.59660.08530.02260.43250.0640.679918.931-30.979-49.812
67.9069-0.79583.8030.8343-0.19692.46520.02380.1506-0.34460.00670.12770.41320.1149-0.0371-0.13970.45-0.02940.01190.35250.12470.632712.7165-29.7593-63.8507
76.12731.01332.63622.36540.7752.18910.05820.2806-0.2931-0.12870.01180.08580.08420.1101-0.11660.3630.02840.00290.3176-0.00710.398632.5318-46.2066-70.1557
88.9872-0.65930.84075.8389-0.50395.76110.45090.63490.8648-0.9098-0.16070.7559-0.0205-0.8432-0.27720.61830.0697-0.13640.4560.0560.6321-2.7391-33.2252-93.0368
96.0959-1.01736.58661.2001-0.51916.890.2672-0.52220.1621-0.0763-0.09210.30680.3175-0.4333-0.28060.372-0.05660.00710.27360.09110.57421.7588-39.7033-70.077
100.69550.15361.82510.81011.10877.5192-0.04740.1944-0.1277-0.3142-0.1360.407-0.2930.05590.19160.5576-0.032-0.05220.52890.02280.569154.8093-15.1404-120.7967
111.0017-0.0090.86922.10390.91222.6435-0.01030.22-0.1399-0.57210.04690.2217-0.67850.0636-0.09130.3976-0.0649-0.03670.52310.0320.467958.8747-12.7932-129.2681
128.1438-1.54922.25221.86870.38021.82080.40980.5963-0.5972-0.2279-0.12030.29940.20880.11-0.32690.5171-0.07780.00670.48450.15020.470636.3863-31.3315-91.7572
133.73071.01652.0805-0.19630.32881.0999-0.2355-0.53311.3469-0.1294-0.12820.1084-0.1848-0.33360.29830.5660.1214-0.09440.52120.02470.634921.9051-20.9979-87.9841
141.94910.04550.06041.39030.48570.67280.0556-0.5781-0.059-0.2269-0.14920.2658-0.0195-0.31320.05290.379-0.01850.01130.4805-0.01570.361823.7933-29.5381-86.4086
156.4326-1.95584.00857.1952-4.9914.65122.1746-0.0528-1.8215-2.0631-1.01312.50471.16650.3187-1.30741.57330.0138-0.25760.8486-0.07941.35255.089-41.1101-166.6372
16-1.37540.4932-0.39450.20962.17853.8429-0.11730.06160.017-0.176-0.54660.3693-0.1923-1.58330.97771.01740.1574-0.18661.2186-0.14920.650457.5012-38.4227-127.8541
177.11152.04691.61794.87962.26418.08670.02150.3592-0.7271-0.1871-0.14770.00350.773-0.11880.1280.48070.07450.07570.3308-0.00740.454769.7256-36.8951-104.8227
184.72721.6543-4.03682.2901-1.7933.254-0.20570.1584-0.1161-0.3904-0.21810.0201-0.56550.42620.55741.29620.0634-0.13680.3822-0.05390.452467.0797-32.4964-159.5589
190.09550.1438-0.97031.2890.87482.4511-0.22720.0622-0.0096-0.1744-0.20030.2374-0.9604-0.68010.56730.51870.0705-0.08560.5617-0.04120.468862.8947-29.9623-121.05
200.4902-0.48161.54280.9511-2.04457.82170.0920.0791-0.0033-0.37930.03940.00391.07210.2846-0.15580.76470.0268-0.10210.4633-0.04820.56788.7994-37.5996-128.8687
210.7025-0.45411.9070.2602-1.2553.3799-0.42130.27320.3294-0.4501-0.2754-0.1105-0.41580.46710.7351.0738-0.0438-0.03130.52820.01360.529183.6402-24.1873-139.6916
221.2656-0.35561.69961.75810.05732.62790.0958-0.0232-0.0169-0.20720.10680.03740.49380.0853-0.1430.5813-0.0229-0.06990.3374-0.00890.459679.637-31.9851-133.4074
230.0720.29070.8544.07235.38399.7213-0.28681.30230.9241-1.4734-0.0421-1.1047-0.42180.62980.35881.2915-0.08260.13511.2580.23530.937282.1271-4.9494-169.2453
246.814-4.79965.59133.216-3.86584.10080.31050.1796-0.4005-0.26770.21060.14760.53260.8733-0.42660.89540.06140.01470.6483-0.08370.619493.9833-11.2474-140.4821
253.368-1.11142.59262.68060.90223.3676-0.2366-0.05380.4141-0.264-0.0352-1.23490.53731.22620.75650.59770.11450.06750.7355-0.12580.7324107.4578-14.5971-114.1502
264.3419-2.7592-3.99954.9994.92059.127-0.1184-0.44670.24580.07250.4647-0.3849-0.12110.809-0.27080.5973-0.0248-0.06770.4199-0.06370.50397.0804-8.059-106.5676
275.5903-1.40093.70623.0088-0.15952.8041-0.2040.47080.2015-0.6128-0.0732-0.292-0.5273-0.79080.38380.6396-0.0287-0.03660.3688-0.02810.470689.4355-9.0486-116.9306
288.6793-1.34885.75810.0692-1.12818.4988-0.23820.19580.5398-0.5864-0.3948-0.0413-0.6083-0.33650.45741.4143-0.0894-0.22880.52160.02620.74569.7553-6.7562-160.2811
292.55560.00533.0091.3147-0.19424.07410.39520.2781-0.2761-0.33550.2094-0.04620.45190.5791-0.71160.6454-0.03190.04070.3412-0.06450.468687.1686-15.9282-133.2915
304.7432-0.06565.52182.3170.11368.7879-0.30040.4120.1748-0.449-0.02640.3071-0.42910.10480.46950.6704-0.0556-0.02930.45780.04360.437373.978.0778-127.0704
315.8142.2536-3.42445.1283-4.9835.1940.2902-0.58840.0041.05820.07420.616-1.0789-0.0651-0.33470.54060.0459-0.05850.5656-0.05150.440675.66951.5975-100.4847
328.2446-3.52747.12817.8621-6.33118.58730.55910.1172-0.042-0.91080.48951.13130.9836-1.3961-0.87150.4667-0.0461-0.06930.52990.01240.468472.0897-3.1124-112.0911
334.60660.17431.39181.1319-1.41182.4663-0.63160.68040.471-1.1131-0.17860.94040.5117-0.62250.73151.2974-0.0794-0.51930.8097-0.06390.841855.4652-8.7819-156.0434
344.12860.65024.80641.73681.20324.3451-0.27430.31990.0912-0.38020.0860.1264-0.45390.28980.20880.5141-0.05590.00980.3464-0.01220.384275.0382-2.039-129.5183
356.1403-0.55560.52920.0646-0.8611-0.87320.46621.50920.3679-0.2133-0.30290.06370.08840.0767-0.15790.59980.1032-0.16141.0193-0.18070.811211.9692-3.1657-91.2804
366.31850.57061.41934.7727-1.18776.6494-0.17410.0560.5484-0.1079-0.0667-0.0158-0.6424-0.12240.30360.35240.00880.02320.3113-0.00860.443147.7639-5.8162-75.0293
374.81542.859-3.77784.0777-1.58774.08181.2138-0.4139-0.2723-0.0168-0.63040.33870.1077-0.1516-0.41090.46840.069-0.19550.4865-0.02711.0128-7.9126-9.7219-82.7039
388.9456-0.17271.69240.7669-0.08460.71660.03480.1947-0.175-0.0363-0.04340.1378-0.05740.0053-0.0690.42120.0003-0.06060.48150.03480.545531.0254-12.465-82.9443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 10 through 105 )
2X-RAY DIFFRACTION2chain 'B' and (resid 106 through 129 )
3X-RAY DIFFRACTION3chain 'B' and (resid 130 through 170 )
4X-RAY DIFFRACTION4chain 'B' and (resid 171 through 234 )
5X-RAY DIFFRACTION5chain 'C' and (resid 11 through 105 )
6X-RAY DIFFRACTION6chain 'C' and (resid 106 through 232 )
7X-RAY DIFFRACTION7chain 'D' and (resid 19 through 129 )
8X-RAY DIFFRACTION8chain 'D' and (resid 130 through 166 )
9X-RAY DIFFRACTION9chain 'D' and (resid 167 through 233 )
10X-RAY DIFFRACTION10chain 'E' and (resid 19 through 159 )
11X-RAY DIFFRACTION11chain 'E' and (resid 160 through 234 )
12X-RAY DIFFRACTION12chain 'F' and (resid 12 through 105 )
13X-RAY DIFFRACTION13chain 'F' and (resid 106 through 159 )
14X-RAY DIFFRACTION14chain 'F' and (resid 160 through 234 )
15X-RAY DIFFRACTION15chain 'G' and (resid 7 through 20 )
16X-RAY DIFFRACTION16chain 'G' and (resid 21 through 67 )
17X-RAY DIFFRACTION17chain 'G' and (resid 68 through 129 )
18X-RAY DIFFRACTION18chain 'G' and (resid 130 through 170 )
19X-RAY DIFFRACTION19chain 'G' and (resid 171 through 235 )
20X-RAY DIFFRACTION20chain 'H' and (resid 10 through 105 )
21X-RAY DIFFRACTION21chain 'H' and (resid 106 through 161 )
22X-RAY DIFFRACTION22chain 'H' and (resid 162 through 234 )
23X-RAY DIFFRACTION23chain 'I' and (resid 10 through 21 )
24X-RAY DIFFRACTION24chain 'I' and (resid 22 through 63 )
25X-RAY DIFFRACTION25chain 'I' and (resid 64 through 82 )
26X-RAY DIFFRACTION26chain 'I' and (resid 83 through 105 )
27X-RAY DIFFRACTION27chain 'I' and (resid 106 through 129 )
28X-RAY DIFFRACTION28chain 'I' and (resid 130 through 166 )
29X-RAY DIFFRACTION29chain 'I' and (resid 167 through 232 )
30X-RAY DIFFRACTION30chain 'J' and (resid 19 through 82 )
31X-RAY DIFFRACTION31chain 'J' and (resid 83 through 105 )
32X-RAY DIFFRACTION32chain 'J' and (resid 106 through 129 )
33X-RAY DIFFRACTION33chain 'J' and (resid 130 through 167 )
34X-RAY DIFFRACTION34chain 'J' and (resid 168 through 232 )
35X-RAY DIFFRACTION35chain 'A' and (resid 2 through 64 )
36X-RAY DIFFRACTION36chain 'A' and (resid 65 through 129 )
37X-RAY DIFFRACTION37chain 'A' and (resid 130 through 170 )
38X-RAY DIFFRACTION38chain 'A' and (resid 171 through 234 )

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